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Basic information

Entry
Database: PDB / ID: 3wtp
TitleCrystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3
Components
  • DNA (146-MER)
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3-like centromeric protein A
  • Histone H3.3
  • Histone H4
KeywordsDNA BINDING PROTEIN/DNA / histone fold / DNA binding / chromatin formation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


CENP-A containing chromatin assembly / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation ...CENP-A containing chromatin assembly / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / nucleosomal DNA binding / nucleus organization / spermatid development / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / single fertilization / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Resolution of Sister Chromatid Cohesion / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / male gonad development / osteoblast differentiation / structural constituent of chromatin / Separation of Sister Chromatids / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence
Similarity search - Function
Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A ...Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H3-like centromeric protein A / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsArimura, Y. / Shirayama, K. / Horikoshi, N. / Fujita, R. / Kagawa, W. / Fukagawa, T. / Almouzni, G. / Kurumizaka, H.
CitationJournal: Sci Rep / Year: 2014
Title: Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3
Authors: Arimura, Y. / Shirayama, K. / Horikoshi, N. / Fujita, R. / Taguchi, H. / Kagawa, W. / Fukagawa, T. / Almouzni, G. / Kurumizaka, H.
History
DepositionApr 14, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3-like centromeric protein A
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.3
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)202,80810
Polymers202,80810
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55440 Å2
ΔGint-392 kcal/mol
Surface area72390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.117, 107.667, 168.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 5 types, 8 molecules ABFCGDHE

#1: Protein Histone H3-like centromeric protein A / Centromere autoantigen A / Centromere protein A / CENP-A


Mass: 16305.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P49450
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3.3, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, ...Gene: H3.3, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AFA, H2AFM, H4, HIST1H2AB, HIST1H2AE / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14217.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2A, H2BFR, HIST1H2BJ / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06899
#5: Protein Histone H3.3


Mass: 15710.351 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781 / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84243

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DNA chain , 1 types, 2 molecules IJ

#6: DNA chain DNA (146-MER)


Mass: 45053.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97319 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97319 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. all: 51813 / Num. obs: 50779 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 49.15 Å2 / Rsym value: 0.1 / Χ2: 1.049 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.67-2.793.12.757400.3811.09790
2.79-2.944.33.662630.3591.08898.2
2.94-3.124.84.963260.2811.06998.9
3.12-3.365.47.363530.1951.01899.1
3.36-3.76.111.164030.1381.02699.5
3.7-4.246.515.664400.1031.08699.7
4.24-5.346.820.465150.0781.0299.8
5.34-506.824.867390.0611.0499

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2cv5

2cv5


Resolution: 2.67→48.667 Å / FOM work R set: 0.8163 / SU ML: 0.42 / σ(F): 1.48 / Phase error: 26.34 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 2558 5.07 %RANDOM
Rwork0.2285 ---
obs0.2306 50416 98.26 %-
all-50743 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.69 Å2 / Biso mean: 55.43 Å2 / Biso min: 13.2 Å2
Refinement stepCycle: LAST / Resolution: 2.67→48.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 5980 0 0 11916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812727
X-RAY DIFFRACTIONf_angle_d1.00518440
X-RAY DIFFRACTIONf_chiral_restr0.052096
X-RAY DIFFRACTIONf_plane_restr0.0051318
X-RAY DIFFRACTIONf_dihedral_angle_d28.5675229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.67-2.72140.36051230.3323232446232387
2.7214-2.77690.38631450.327725192664251994
2.7769-2.83730.3491470.314525802727258098
2.8373-2.90330.311640.290126282792262898
2.9033-2.97590.32371350.278726292764262998
2.9759-3.05630.34281460.267426052751260599
3.0563-3.14630.28021270.256426902817269099
3.1463-3.24780.28581290.256726682797266899
3.2478-3.36380.3121190.24626952814269599
3.3638-3.49850.26081630.222726482811264899
3.4985-3.65770.2261480.2191266728152667100
3.6577-3.85040.26041250.2203271628412716100
3.8504-4.09160.25611340.2091270828422708100
4.0916-4.40730.24551590.2013269528542695100
4.4073-4.85040.24291430.2057272328662723100
4.8504-5.55150.25821300.2089275528852755100
5.5515-6.99090.29421560.2293277429302774100
6.9909-48.67520.22561650.187128353000283598

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